A primer on phylogenetic generalised least squares

Symonds,MRE and Blomberg,SP 2014, A primer on phylogenetic generalised least squares. In Zsolt Garamszegi,L (ed), Modern phylogenetic comparative methods and their application in evolutionary biology : concepts and practice, Springer, Berlin, Germany, pp.105-130, doi: 10.1007/978-3-662-43550-2_5.

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Title A primer on phylogenetic generalised least squares
Author(s) Symonds,MREORCID iD for Symonds,MRE orcid.org/0000-0002-9785-6045
Title of book Modern phylogenetic comparative methods and their application in evolutionary biology : concepts and practice
Editor(s) Zsolt Garamszegi,L
Publication date 2014
Chapter number 5
Total chapters 22
Start page 105
End page 130
Total pages 26
Publisher Springer
Place of Publication Berlin, Germany
Summary Phylogenetic generalised least squares (PGLS) is one of the most commonly employed phylogenetic comparative methods. The technique, a modification of generalised least squares, uses knowledge of phylogenetic relationships to produce an estimate of expected covariance in cross-species data. Closely related species are assumed to have more similar traits because of their shared ancestry and hence produce more similar residuals from the least squares regression line. By taking into account the expected covariance structure of these residuals, modified slope and intercept estimates are generated that can account for interspecific autocorrelation due to phylogeny. Here, we provide a basic conceptual background to PGLS, for those unfamiliar with the approach. We describe the requirements for a PGLS analysis and highlight the packages that can be used to implement the method. We show how phylogeny is used to calculate the expected covariance structure in the data and how this is applied to the generalised least squares regression equation. We demonstrate how PGLS can incorporate information about phylogenetic signal, the extent to which closely related species truly are similar, and how it controls for this signal appropriately, thereby negating concerns about unnecessarily ‘correcting’ for phylogeny. In addition to discussing the appropriate way to present the results of PGLS analyses, we highlight some common misconceptions about the approach and commonly encountered problems with the method. These include misunderstandings about what phylogenetic signal refers to in the context of PGLS (residuals errors, not the traits themselves), and issues associated with unknown or uncertain phylogeny.
ISBN 9783662435496
Language eng
DOI 10.1007/978-3-662-43550-2_5
Field of Research 060309 Phylogeny and Comparative Analysis
Socio Economic Objective 970106 Expanding Knowledge in the Biological Sciences
HERDC Research category B1 Book chapter
ERA Research output type B Book chapter
Copyright notice ©2014, Springer
Persistent URL http://hdl.handle.net/10536/DRO/DU:30071705

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